[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

fnothaft · 2016-07-06T19:06:59Z

Resolves #1006.

heuermh · 2016-07-06T19:11:42Z

adam-assembly/pom.xml

+ </dependency>
+ </dependencies>
+ <profiles>
+ <profile>


this can be removed

AmplabJenkins · 2016-07-06T19:11:51Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 2b8b12b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains ec68563af086f51e3ee289e9f645153c0b557b30 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision ec68563af086f51e3ee289e9f645153c0b557b30 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ec68563af086f51e3ee289e9f645153c0b557b30First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T19:16:46Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 96e31c2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6ac9206 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 6ac9206 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6ac9206c42d241aeed4cb66c8b64da62fe97633aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T20:02:29Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #1072 of commit f1f502f.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse f1f502f^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f1f502f # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/head^{commit} # timeout=10Checking out Revision f1f502f (origin/pr/1072/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f1f502f484c72e89b59e738d216648981954e423First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T20:12:50Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 911f1bd automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4719ef49d194aab7b40067fabbb61f67c5071fb7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 4719ef49d194aab7b40067fabbb61f67c5071fb7 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4719ef49d194aab7b40067fabbb61f67c5071fb7First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T20:42:42Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #1072 of commit de1e4ea automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 21c5be163baf13c96f7ee8474d9467adf4f8ef31 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 21c5be163baf13c96f7ee8474d9467adf4f8ef31 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 21c5be163baf13c96f7ee8474d9467adf4f8ef31 > /home/jenkins/git2/bin/git rev-list 4719ef49d194aab7b40067fabbb61f67c5071fb7 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-06T21:27:21Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-06T21:43:30Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1313/

Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-06T21:48:29Z

Jenkins, retest this please.

fnothaft · 2016-07-06T21:56:56Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-06T22:15:21Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T22:40:35Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-07T01:13:44Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-07T01:37:32Z

Test PASSed.
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Test PASSed.

fnothaft · 2016-07-07T03:17:34Z

@heuermh I believe this is good to go.

heuermh · 2016-07-07T13:28:31Z

bin/adam-submit

 if [ "$num_jars" -eq "0" ]; then
 echo "Failed to find ADAM cli assembly in $ASSEMBLY_DIR." 1>&2
 echo "You need to build ADAM before running this program." 1>&2
 exit 1
 fi

-ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"
+ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"


I wonder if it might be preferable to use <finalName>adam_2.10</finalName> for the fat jar artifact?

I'm agnostic. LMK your preference.

AmplabJenkins · 2016-07-07T13:57:28Z

Test FAILed.
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-07T14:42:36Z

Got the finalName patch in.

AmplabJenkins · 2016-07-07T15:00:30Z

Test PASSed.
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Test PASSed.

heuermh · 2016-07-07T20:35:28Z

Merged commit 48302d9

Thank you, @fnothaft!

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 2b8b12b to 96e31c2 Compare July 6, 2016 19:10

heuermh reviewed Jul 6, 2016
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adam-assembly/pom.xml

</dependency>

</dependencies>

<profiles>

<profile>

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this can be removed

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 96e31c2 to f1f502f Compare July 6, 2016 19:57

fnothaft force-pushed the issues/1006-separate-fat-jar branch from f1f502f to 911f1bd Compare July 6, 2016 20:03

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 911f1bd to de1e4ea Compare July 6, 2016 20:34

heuermh reviewed Jul 7, 2016
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fnothaft force-pushed the issues/1006-separate-fat-jar branch 2 times, most recently from 6d8dd3e to 397c113 Compare July 7, 2016 13:37

[ADAM-1006] Split uberjar out to adam-assembly submodule.

48302d9

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 397c113 to 48302d9 Compare July 7, 2016 14:42

heuermh closed this Jul 7, 2016

heuermh mentioned this pull request Jul 7, 2016

Separate fat jar build from adam-cli to new maven module #1006

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[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

fnothaft commented Jul 6, 2016

heuermh Jul 6, 2016

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heuermh Jul 7, 2016

fnothaft Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

fnothaft commented Jul 7, 2016

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heuermh commented Jul 7, 2016

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

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AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 6, 2016

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 6, 2016

fnothaft commented Jul 6, 2016

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

fnothaft commented Jul 7, 2016

heuermh Jul 7, 2016

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fnothaft Jul 7, 2016

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AmplabJenkins commented Jul 7, 2016

Build result: FAILURE

fnothaft commented Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

heuermh commented Jul 7, 2016